Hi Thomas, First it is important to compare equivalent major versions to each other. Particularly in this case. On my linux box generating the pattern fingerprints takes 24.2 seconds with v2019.03.x and 15.9 seconds with v2019.09.x (that's due to the improvements in the substructure matcher that the blog post you link to discusses).
Comparing the same versions to each other: Performance on windows vs linux Windows performance with the RDKit has always lagged behind linux performance. There's something in the code (or in the way we use the compiler) that leads to big differences on some benchmarks. The most straightforward way I can demonstrate this is with results from my windows 10 laptop. Here's the output when running the fingerprint_screenout.py benchmark using the windows build: | 2019.09.1 | 13.6 | 0.3 | 38.1 | 0.8 | 25.5 | 25.9 | 84.1 | and here's the output from a linux build running on the Windows Linux Subsystem: | 2019.09.2 | 10.7 | 0.2 | 19.3 | 0.4 | 19.4 | 19.2 | 53.2 | You can see the differences are not small. I haven't invested massive time into it, but I haven't been able to figure out what causes this. Performance on (linux) VMs I can't think of any particular reason why there should be huge differences and it's really difficult to compare apples to apples here. Since I have the numbers, here's one comparison Here's a run on my linux workstation: | 2019.09.2 | 7.6 | 0.3 | 15.9 | 0.4 | 21.4 | 20.4 | 55.7 | and here's the same thing on an AWS t3.xlarge instance: | 2019.09.2 | 9.6 | 0.2 | 20.3 | 0.4 | 38.4 | 38.2 | 94.7 | The VM is significantly slower, but t3.xlarge an instance type that's intended to be used for compute intensive jobs (I don't have on of those active and configured at the moment). Does that help at all? -greg On Mon, Dec 16, 2019 at 8:27 AM Thomas Strunz <beginn...@hotmail.de> wrote: > Hi All, > > I was looking at a blog post from greg: > > > https://rdkit.blogspot.com/2019/07/a-couple-of-substructure-search-topics.html > > about fingerprint screenout. The part that got me confused was the timings > in his blog post because run times in my case where a lot slower. > > Gregs numbers: > > [07:21:19] INFO: mols from smiles > [07:21:27] INFO: Results1: 7.77 seconds, 50000 mols > [07:21:27] INFO: queries from smiles > [07:21:27] INFO: Results2: 0.16 seconds*[07:21:27] INFO: generating pattern > fingerprints for mols > [07:21:43] INFO: Results3: 16.11 seconds* > [07:21:43] INFO: generating pattern fingerprints for queries > [07:21:43] INFO: Results4: 0.34 seconds > [07:21:43] INFO: testing frags queries > [07:22:03] INFO: Results5: 19.90 seconds. 6753 tested (0.0003 of total), > 3989 found, 0.59 accuracy. 0 errors. > [07:22:03] INFO: testing leads queries > [07:22:23] INFO: Results6: 19.77 seconds. 1586 tested (0.0001 of total), > 1067 found, 0.67 accuracy. 0 errors. > [07:22:23] INFO: testing pieces queries > [07:23:19] INFO: Results7: 55.37 seconds. 3333202 tested (0.0810 of total), > 1925628 found, 0.58 accuracy. 0 errors. > > | 2019.09.1dev1 | 7.8 | 0.2 | 16.1 | 0.3 | 19.9 | 19.8 | 55.4 | > > > > > *Machine 1:* > Virtual machine, Windows Server 2012 R2 with an intel xeon (4 virtual > cores) > > Since the test is single-threaded it makes a bit of sense that it isn't > fast here but it's not just a bit slower, but a lot slower, depending on > test almost 3xtimes slower > > [09:03:19] INFO: mols from smiles > [09:03:38] INFO: Results1: 19.44 seconds, 50000 mols > [09:03:38] INFO: queries from smiles > [09:03:38] INFO: Results2: 0.36 seconds > > *[09:03:38] INFO: generating pattern fingerprints for mols * > *[09:04:54] INFO: Results3: 75.99 seconds* > [09:04:54] INFO: generating pattern fingerprints for queries > [09:04:56] INFO: Results4: 1.55 seconds > [09:04:56] INFO: testing frags queries > [09:05:34] INFO: Results5: 37.59 seconds. 6753 tested (0.0003 of total), > 3989 f > ound, 0.59 accuracy. 0 errors. > [09:05:34] INFO: testing leads queries > [09:06:11] INFO: Results6: 37.34 seconds. 1586 tested (0.0001 of total), > 1067 f > ound, 0.67 accuracy. 0 errors. > [09:06:11] INFO: testing pieces queries > [09:08:39] INFO: Results7: 147.79 seconds. 3333202 tested (0.0810 of > total), 19 > 25628 found, 0.58 accuracy. 0 errors. > | 2019.03.3 | 19.4 | 0.4 | 76.0 | 1.5 | 37.6 | 37.3 | 147.8 | > > I thought maybe another issue with windows being slow so I tested on a > linux VM on my laptop > > *Machine 2:* > Virtual machine, Lubuntu 16.04 on a laptop i7-8850H 6-core > > [09:23:31] INFO: mols from smiles > [09:23:54] INFO: Results1: 23.71 seconds, 50000 mols > [09:23:54] INFO: queries from smiles > [09:23:55] INFO: Results2: 0.48 seconds > > *[09:23:55] INFO: generating pattern fingerprints for mols * > *[09:24:53] INFO: Results3: 58.31 seconds* > [09:24:53] INFO: generating pattern fingerprints for queries > [09:24:54] INFO: Results4: 1.19 seconds > [09:24:54] INFO: testing frags queries > [09:25:41] INFO: Results5: 46.22 seconds. 6753 tested (0.0003 of total), > 3989 found, 0.59 accuracy. 0 errors. > [09:25:41] INFO: testing leads queries > [09:26:26] INFO: Results6: 45.84 seconds. 1586 tested (0.0001 of total), > 1067 found, 0.67 accuracy. 0 errors. > [09:26:26] INFO: testing pieces queries > [09:28:33] INFO: Results7: 126.78 seconds. 3333202 tested (0.0810 of > total), 1925628 found, 0.58 accuracy. 0 errors. > | 2019.03.3 | 23.7 | 0.5 | 58.3 | 1.2 | 46.2 | 45.8 | 126.8 | > > Pretty weird sometimes even slower sometimes faster than the windows VM > but still a lot slower than Gregs numbers (I repeated with rdkit 2019.09.2 > and got comparable results) > > So I also tested on above laptop directly: > > *Machine 3:* > physical install, windows 10 on a laptop i7-8850H 6-core (same machine as > 2) > > [09:51:43] INFO: mols from smiles > [09:51:54] INFO: Results1: 10.59 seconds, 50000 mols > [09:51:54] INFO: queries from smiles > [09:51:54] INFO: Results2: 0.20 seconds > > *[09:51:54] INFO: generating pattern fingerprints for mols * > *[09:52:24] INFO: Results3: 29.50 seconds* > [09:52:24] INFO: generating pattern fingerprints for queries > [09:52:24] INFO: Results4: 0.61 seconds > [09:52:24] INFO: testing frags queries > [09:52:44] INFO: Results5: 19.71 seconds. 6753 tested (0.0003 of total), > 3989 found, 0.59 accuracy. 0 errors. > [09:52:44] INFO: testing leads queries > [09:53:04] INFO: Results6: 19.48 seconds. 1586 tested (0.0001 of total), > 1067 found, 0.67 accuracy. 0 errors. > [09:53:04] INFO: testing pieces queries > [09:54:05] INFO: Results7: 61.94 seconds. 3333202 tested (0.0810 of > total), 1925628 found, 0.58 accuracy. 0 errors. > | 2019.09.1 | 10.6 | 0.2 | 29.5 | 0.6 | 19.7 | 19.5 | 61.9 | > > This is much closer to Gregs results, except for the fingerprinting which > takes almost double the time. Also notice how the fingerprinting on the > linux VM is much faster also compared to other results than on the windows > VM? > > *Conclusions:* > > 1. Form what I see, it seems that the pattern fingerprinter runs a lot > slower on windows. Is this known issue? > 2. In virtual machines the rdkits performance simply tanks, is much > worse. A certain penalty is to be expected but not this much. Or what am I > missing? Machine 1 runs on central infrastructure so I would assume > virtualization is configured correctly. For the local VM, vt-x is enabled. > Yet it is much slower compared to the physical machine (plus that AFAIK > rdkit runs faster in linux vs windows) > > Especially the virtual machine aspect is kind of troubling because I would > assume many real-world applications are deployed as VM and hence might > suffer from this too? > I don't have a well defined question but more interested in other users > experience especially regarding the virtualization. > > Best Regards, > > Thomas > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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